Natural Exon Skipping Sets the Stage for Exon Skipping as Therapy for Dystrophic Epidermolysis Bullosa

Abstract

Dystrophic epidermolysis bullosa (DEB) is a devastating blistering disease affecting skin and mucous membranes. It is caused by pathogenic variants in the COL7A1 gene encoding type VII collagen, and can be inherited dominantly or recessively. Recently, promising proof-of-principle has been shown for antisense oligonucleotide (AON)-mediated exon skipping as a therapeutic approach for DEB. However, the precise phenotypic effect to be anticipated from exon skipping, and which patient groups could benefit, is not yet clear. To answer these questions, we studied new clinical and molecular data on seven patients from the Dutch EB registry and reviewed the literature on COL7A1 exon skipping variants. We found that phenotypes associated with dominant exon skipping cannot be distinguished from phenotypes caused by other dominant DEB variants. Recessive exon skipping phenotypes are generally relatively mild in the spectrum of recessive DEB. Therefore, for dominant DEB, AON-mediated exon skipping is unlikely to ameliorate the phenotype. In contrast, the overall severity of phenotypes associated with recessive natural exon skipping pivots toward the milder end of the spectrum. Consequently, we anticipate AON-mediated exon skipping for recessive DEB caused by bi-allelic null variants should lead to a clinically relevant improvement of this devastating phenotype.

Keywords: dystrophic epidermolysis bullosa; exon skipping; genotype-phenotype correlation; splicing; therapy.

Figure 1

Clinical and Molecular Phenotypes of Seven DEB Patients Associated with Natural Exon Skipping Left column: DEB clinical phenotypes associated with natural exon skipping depicted by representative photographs of the hands. Immunofluorescence (IF) staining (×40) of type VII collagen at the basement membrane zone (BMZ) is shown compared with control (middle columns). Right column: IF detail of the BMZ revealing retention of type VII collagen by basal keratinocytes (asterisks) in patients 1–4 and 6. Scale bars: 25 μm.

Figure 2

Overview of the COL7A1 Gene and Natural Exon Skipping Variants The upper pane shows an overview of the type VII collagen protein with the noncollagenous-1 (NC1), triple-helix (THD), and noncollagenous-2 domains (NC2). Dominant and recessive variants leading to natural exon skipping are indicated above and below the pane, respectively. Interruptions of the Gly-X-Y structure are indicated in gray to scale. The NC-2 cleavage site is indicated (scissors). In the middle pane, the upper bar shows all 118 exons to scale with the corresponding nucleotide (Nt) and amino acid (AA) numbers; colors correspond to the respective protein domains encoded. The second bar shows the same exon structure of COL7A1 to scale, this time indicating the exons involved in natural exon skipping (black), other in-frame exon skipping candidates (white), and “non-skippable,” out-of-frame exons (gray). The lower pane shows the relative location of crucial domains. CMP, cartilage-matrix protein motif; C/P cysteine/proline-rich motif; FN-III, fibronectin-III-like domains 1–9; hinge, intrinsically disordered hinge region; KM, Kunitz-motif-like domain; SP, signal peptide; VWA, von Willebrand factor A-like domain.

Figure 3

Variants Causing Natural Exon 87 Skipping Exon 87 and its flanking intronic sequences showing variants that cause natural exon skipping in red. Predicted binding strength of exonic splice enhancers is shown in the lower graph. AU, arbitrary units.